There's currently no diplomacy in the 4X sense of talking to other faction leaders and making specific proposals (partly because most factions don't have leaders to talk to, but mostly because it's Work).
Diplomacy content falls into a few categories:
- random and semi-random events that happen periodically
- specific things that you can respond to (e.g. ceasefire offers by other factions)
- things you can control actively (the aforementioned alliances)
The vanilla methods of modifying reputation still work, and Nexerelin adds some (notably prisoners, aka "reputation coupons earned through combat"). Gifting planets and stations you conquer is also a significant component.